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Marco Lenoir
MarcoTheBlack/
deepvariant
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# Copyright 2019 Google LLC.





  
  

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# This is used to build the DeepVariant release docker image.





  
  

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# It can also be used to build local images, especially if you've made changes





  
  

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# to the code.





  
  

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# Example command:





  
  

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# $ git clone https://github.com/google/deepvariant.git





  
  

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# $ cd deepvariant





  
  

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# $ sudo docker build -t deepvariant .





  
  

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#





  
  

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# To build for GPU, use a command like:





  
  

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# $ sudo docker build --build-arg=FROM_IMAGE=nvidia/cuda:11.8.0-cudnn8-devel-ubuntu22.04 --build-arg=DV_GPU_BUILD=1 -t deepvariant_gpu .





  
  

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ARG FROM_IMAGE=ubuntu:22.04





  
  

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# PYTHON_VERSION is also set in settings.sh.





  
  

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ARG PYTHON_VERSION=3.10





  
  

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ARG DV_GPU_BUILD=0





  
  

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ARG VERSION=1.8.0





  
  

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ARG TF_ENABLE_ONEDNN_OPTS=1





  
  

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FROM continuumio/miniconda3 as conda_setup





  
  

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RUN conda config --add channels defaults && \





  
  

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    conda config --add channels bioconda && \





  
  

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    conda config --add channels conda-forge





  
  

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RUN conda create -n bio \





  
  

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                    bioconda::bcftools=1.15 \





  
  

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                    bioconda::samtools=1.15 \





  
  

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    && conda clean -a





  
  

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FROM ${FROM_IMAGE} as builder





  
  

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COPY --from=conda_setup /opt/conda /opt/conda





  
  

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LABEL maintainer="https://github.com/google/deepvariant/issues"





  
  

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ARG DV_GPU_BUILD





  
  

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ENV DV_GPU_BUILD=${DV_GPU_BUILD}





  
  

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ENV DV_BIN_PATH=/opt/deepvariant/bin





  
  

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# Copying DeepVariant source code





  
  

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COPY . /opt/deepvariant





  
  

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ARG VERSION





  
  

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ENV VERSION=${VERSION}





  
  

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WORKDIR /opt/deepvariant





  
  

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RUN echo "Acquire::http::proxy \"$http_proxy\";\n" \





  
  

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         "Acquire::https::proxy \"$https_proxy\";" > "/etc/apt/apt.conf"





  
  

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RUN ./build-prereq.sh \





  
  

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  && PATH="${HOME}/bin:${PATH}" ./build_release_binaries.sh  # PATH for bazel





  
  

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FROM ${FROM_IMAGE}





  
  

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ARG DV_GPU_BUILD





  
  

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ARG VERSION





  
  

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ARG PYTHON_VERSION





  
  

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ARG TF_ENABLE_ONEDNN_OPTS





  
  

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ENV DV_GPU_BUILD=${DV_GPU_BUILD}





  
  

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ENV VERSION ${VERSION}





  
  

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ENV PYTHON_VERSION ${PYTHON_VERSION}





  
  

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ENV TF_ENABLE_ONEDNN_OPTS ${TF_ENABLE_ONEDNN_OPTS}





  
  

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RUN echo "Acquire::http::proxy \"$http_proxy\";\n" \





  
  

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         "Acquire::https::proxy \"$https_proxy\";" > "/etc/apt/apt.conf"





  
  

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WORKDIR /opt/





  
  

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COPY --from=builder /opt/deepvariant/bazel-bin/licenses.zip .





  
  

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WORKDIR /opt/deepvariant/bin/





  
  

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COPY --from=builder /opt/conda /opt/conda





  
  

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COPY --from=builder /opt/deepvariant/run-prereq.sh .





  
  

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COPY --from=builder /opt/deepvariant/settings.sh .





  
  

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COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/make_examples.zip  .





  
  

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COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/call_variants.zip  .





  
  

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COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/postprocess_variants.zip  .





  
  

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COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/vcf_stats_report.zip  .





  
  

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COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/show_examples.zip  .





  
  

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COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/runtime_by_region_vis.zip  .





  
  

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COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/multisample_make_examples.zip  .





  
  

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COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/labeler/labeled_examples_to_vcf.zip  .





  
  

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COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/make_examples_somatic.zip  .





  
  

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COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/train.zip  .





  
  

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COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/fast_pipeline .





  
  

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COPY --from=builder /opt/deepvariant/scripts/run_deepvariant.py .





  
  

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COPY --from=builder /opt/deepvariant/scripts/run_deepsomatic.py .





  
  

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RUN ./run-prereq.sh





  
  

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RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python${PYTHON_VERSION} 0 && \





  
  

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    update-alternatives --install /usr/bin/python python /usr/bin/python${PYTHON_VERSION} 0





  
  

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# Create shell wrappers for python zip files for easier use.





  
  

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RUN \





  
  

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  BASH_HEADER='#!/bin/bash' && \





  
  

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  printf "%s\n%s\n" \





  
  

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    "${BASH_HEADER}" \





  
  

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    'python3 /opt/deepvariant/bin/make_examples.zip "$@"' > \





  
  

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    /opt/deepvariant/bin/make_examples && \





  
  

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  printf "%s\n%s\n" \





  
  

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    "${BASH_HEADER}" \





  
  

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    'python3 /opt/deepvariant/bin/call_variants.zip "$@"' > \





  
  

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    /opt/deepvariant/bin/call_variants && \





  
  

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  printf "%s\n%s\n" \





  
  

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    "${BASH_HEADER}" \





  
  

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    'python3 /opt/deepvariant/bin/postprocess_variants.zip "$@"' > \





  
  

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    /opt/deepvariant/bin/postprocess_variants && \





  
  

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  printf "%s\n%s\n" \





  
  

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    "${BASH_HEADER}" \





  
  

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    'python3 /opt/deepvariant/bin/vcf_stats_report.zip "$@"' > \





  
  

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    /opt/deepvariant/bin/vcf_stats_report && \





  
  

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  printf "%s\n%s\n" \





  
  

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    "${BASH_HEADER}" \





  
  

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    'python3 /opt/deepvariant/bin/show_examples.zip "$@"' > \





  
  

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    /opt/deepvariant/bin/show_examples && \





  
  

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  printf "%s\n%s\n" \





  
  

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    "${BASH_HEADER}" \





  
  

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    'python3 /opt/deepvariant/bin/runtime_by_region_vis.zip "$@"' > \





  
  

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    /opt/deepvariant/bin/runtime_by_region_vis && \





  
  

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  printf "%s\n%s\n" \





  
  

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    "${BASH_HEADER}" \





  
  

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    'python3 /opt/deepvariant/bin/multisample_make_examples.zip "$@"' > \





  
  

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    /opt/deepvariant/bin/multisample_make_examples && \





  
  

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  printf "%s\n%s\n" \





  
  

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    "${BASH_HEADER}" \





  
  

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    'python3 -u /opt/deepvariant/bin/labeled_examples_to_vcf.zip "$@"' > \





  
  

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    /opt/deepvariant/bin/labeled_examples_to_vcf && \





  
  

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  printf "%s\n%s\n" \





  
  

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    "${BASH_HEADER}" \





  
  

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    'python3 -u /opt/deepvariant/bin/make_examples_somatic.zip "$@"' > \





  
  

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    /opt/deepvariant/bin/make_examples_somatic && \





  
  

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  printf "%s\n%s\n" \





  
  

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    "${BASH_HEADER}" \





  
  

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    'python3 -u /opt/deepvariant/bin/run_deepvariant.py "$@"' > \





  
  

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    /opt/deepvariant/bin/run_deepvariant && \





  
  

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  printf "%s\n%s\n" \





  
  

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    "${BASH_HEADER}" \





  
  

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    'python3 -u /opt/deepvariant/bin/run_deepsomatic.py "$@"' > \





  
  

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    /opt/deepvariant/bin/run_deepsomatic && \





  
  

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  printf "%s\n%s\n" \





  
  

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    "${BASH_HEADER}" \





  
  

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    'python3 /opt/deepvariant/bin/train.zip "$@"' > \





  
  

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    /opt/deepvariant/bin/train && \





  
  

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  chmod +x /opt/deepvariant/bin/make_examples \





  
  

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    /opt/deepvariant/bin/call_variants \





  
  

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    /opt/deepvariant/bin/postprocess_variants \





  
  

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    /opt/deepvariant/bin/vcf_stats_report \





  
  

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    /opt/deepvariant/bin/show_examples \





  
  

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    /opt/deepvariant/bin/runtime_by_region_vis \





  
  

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    /opt/deepvariant/bin/multisample_make_examples \





  
  

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    /opt/deepvariant/bin/run_deepvariant \





  
  

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    /opt/deepvariant/bin/run_deepsomatic \





  
  

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    /opt/deepvariant/bin/labeled_examples_to_vcf \





  
  

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    /opt/deepvariant/bin/make_examples_somatic \





  
  

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    /opt/deepvariant/bin/train





  
  

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# Copy models





  
  

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WORKDIR /opt/models/wgs





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.wgs.savedmodel/fingerprint.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.wgs.savedmodel/saved_model.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.wgs.savedmodel/example_info.json .





  
  

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WORKDIR /opt/models/wgs/variables





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.wgs.savedmodel/variables/variables.data-00000-of-00001 .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.wgs.savedmodel/variables/variables.index .





  
  

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RUN chmod -R +r /opt/models/wgs/*





  
  

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WORKDIR /opt/models/wes





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.wes.savedmodel/fingerprint.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.wes.savedmodel/saved_model.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.wes.savedmodel/example_info.json .





  
  

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WORKDIR /opt/models/wes/variables





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.wes.savedmodel/variables/variables.data-00000-of-00001 .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.wes.savedmodel/variables/variables.index .





  
  

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RUN chmod -R +r /opt/models/wes/*





  
  

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WORKDIR /opt/models/pacbio





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.pacbio.savedmodel/fingerprint.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.pacbio.savedmodel/saved_model.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.pacbio.savedmodel/example_info.json .





  
  

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WORKDIR /opt/models/pacbio/variables





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.pacbio.savedmodel/variables/variables.data-00000-of-00001 .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.pacbio.savedmodel/variables/variables.index .





  
  

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RUN chmod -R +r /opt/models/pacbio/*





  
  

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WORKDIR /opt/models/hybrid_pacbio_illumina





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.hybrid.savedmodel/fingerprint.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.hybrid.savedmodel/saved_model.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.hybrid.savedmodel/example_info.json .





  
  

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WORKDIR /opt/models/hybrid_pacbio_illumina/variables





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.hybrid.savedmodel/variables/variables.data-00000-of-00001 .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.hybrid.savedmodel/variables/variables.index .





  
  

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RUN chmod -R +r /opt/models/hybrid_pacbio_illumina/*





  
  

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WORKDIR /opt/models/ont_r104





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.ont.savedmodel/fingerprint.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.ont.savedmodel/saved_model.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.ont.savedmodel/example_info.json .





  
  

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WORKDIR /opt/models/ont_r104/variables





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.ont.savedmodel/variables/variables.data-00000-of-00001 .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.ont.savedmodel/variables/variables.index .





  
  

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RUN chmod -R +r /opt/models/ont_r104/*





  
  

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WORKDIR /opt/models/masseq





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.masseq.savedmodel/fingerprint.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.masseq.savedmodel/saved_model.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.masseq.savedmodel/example_info.json .





  
  

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WORKDIR /opt/models/masseq/variables





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.masseq.savedmodel/variables/variables.data-00000-of-00001 .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.masseq.savedmodel/variables/variables.index .





  
  

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RUN chmod -R +r /opt/models/masseq/*





  
  

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# Copy small models





  
  

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WORKDIR /opt/smallmodels/wgs





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/smallmodels/deepvariant.wgs.smallmodel/fingerprint.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/smallmodels/deepvariant.wgs.smallmodel/saved_model.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/smallmodels/deepvariant.wgs.smallmodel/keras_metadata.pb .





  
  

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WORKDIR /opt/smallmodels/wgs/variables





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/smallmodels/deepvariant.wgs.smallmodel/variables/variables.data-00000-of-00001 .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/smallmodels/deepvariant.wgs.smallmodel/variables/variables.index .





  
  

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RUN chmod -R +r /opt/smallmodels/wgs/*





  
  

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WORKDIR /opt/smallmodels/pacbio





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/smallmodels/deepvariant.pacbio.smallmodel/fingerprint.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/smallmodels/deepvariant.pacbio.smallmodel/saved_model.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/smallmodels/deepvariant.pacbio.smallmodel/keras_metadata.pb .





  
  

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WORKDIR /opt/smallmodels/pacbio/variables





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/smallmodels/deepvariant.pacbio.smallmodel/variables/variables.data-00000-of-00001 .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/smallmodels/deepvariant.pacbio.smallmodel/variables/variables.index .





  
  

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RUN chmod -R +r /opt/smallmodels/pacbio/*





  
  

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WORKDIR /opt/smallmodels/hybrid_pacbio_illumina





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/smallmodels/deepvariant.hybrid.smallmodel/fingerprint.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/smallmodels/deepvariant.hybrid.smallmodel/saved_model.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/smallmodels/deepvariant.hybrid.smallmodel/keras_metadata.pb .





  
  

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WORKDIR /opt/smallmodels/hybrid_pacbio_illumina/variables





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/smallmodels/deepvariant.hybrid.smallmodel/variables/variables.data-00000-of-00001 .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/smallmodels/deepvariant.hybrid.smallmodel/variables/variables.index .





  
  

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RUN chmod -R +r /opt/smallmodels/hybrid_pacbio_illumina/*





  
  

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WORKDIR /opt/smallmodels/ont_r104





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/smallmodels/deepvariant.ont.smallmodel/fingerprint.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/smallmodels/deepvariant.ont.smallmodel/saved_model.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/smallmodels/deepvariant.ont.smallmodel/keras_metadata.pb .





  
  

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WORKDIR /opt/smallmodels/ont_r104/variables





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/smallmodels/deepvariant.ont.smallmodel/variables/variables.data-00000-of-00001 .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/smallmodels/deepvariant.ont.smallmodel/variables/variables.index .





  
  

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RUN chmod -R +r /opt/smallmodels/ont_r104/*





  
  

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ENV PATH="${PATH}":/opt/conda/bin:/opt/conda/envs/bio/bin:/opt/deepvariant/bin





  
  

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RUN apt-get -y update && \





  
  

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  apt-get install -y parallel python3-pip && \





  
  

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  PATH="${HOME}/.local/bin:$PATH" python3 -m pip install absl-py==0.13.0 && \





  
  

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  apt-get clean autoclean && \





  
  

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  apt-get autoremove -y --purge && \





  
  

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  rm -rf /var/lib/apt/lists/*





  
  

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WORKDIR /opt/deepvariant





  
  

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CMD ["/opt/deepvariant/bin/run_deepvariant", "--help"]